Variant 13-24223195-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001166271.3(SPATA13):c.266G>C(p.Arg89Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000688 in 1,551,636 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0035 ( 2 hom., cov: 33)

Exomes 𝑓: 0.00038 ( 5 hom. )

Consequence

SPATA13
NM_001166271.3 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 8.14

Variant links:

Genes affected

SPATA13 (HGNC:23222): (spermatogenesis associated 13) Enables guanyl-nucleotide exchange factor activity and identical protein binding activity. Involved in cell migration; plasma membrane bounded cell projection assembly; and regulation of cell migration. Located in several cellular components, including filopodium; lamellipodium; and ruffle membrane. [provided by Alliance of Genome Resources, Apr 2022]

SPATA13 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0068299472).

BP6

Variant 13-24223195-G-C is Benign according to our data. Variant chr13-24223195-G-C is described in ClinVar as [Benign]. Clinvar id is 3035879.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd at 539 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
SPATA13	NM_001166271.3 linkuse as main transcript	c.266G>C	p.Arg89Pro	missense_variant	2/13	ENST00000382108.8
SPATA13	NM_001286792.2 linkuse as main transcript	c.452G>C	p.Arg151Pro	missense_variant	4/15
SPATA13	NM_153023.4 linkuse as main transcript	c.-222-26282G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	UniProt
SPATA13	ENST00000382108.8 linkuse as main transcript	c.266G>C	p.Arg89Pro	missense_variant	2/13	5	NM_001166271.3	Q96N96-6
SPATA13	ENST00000424834.6 linkuse as main transcript	c.266G>C	p.Arg89Pro	missense_variant	4/15	1		Q96N96-6
SPATA13	ENST00000382095.8 linkuse as main transcript	c.-222-26282G>C		intron_variant		2		Q96N96-1
SPATA13	ENST00000466831.2 linkuse as main transcript	n.588G>C		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.00354

AC:

539

AN:

152178

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0124

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000982

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000147

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.000825

AC:

129

AN:

156336

Hom.:

AF XY:

0.000712

AC XY:

AN XY:

82910

show subpopulations

Gnomad AFR exome

AF:

0.0146

Gnomad AMR exome

AF:

0.000365

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000331

Gnomad OTH exome

AF:

0.000684

GnomAD4 exome

AF:

0.000377

AC:

528

AN:

1399340

Hom.:

Cov.:

AF XY:

0.000309

AC XY:

213

AN XY:

690170

show subpopulations

Gnomad4 AFR exome

AF:

0.0148

Gnomad4 AMR exome

AF:

0.000476

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000757

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000371

Gnomad4 OTH exome

AF:

0.000569

GnomAD4 genome

AF:

0.00354

AC:

539

AN:

152296

Hom.:

Cov.:

AF XY:

0.00345

AC XY:

257

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.0124

Gnomad4 AMR

AF:

0.000980

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000147

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.000134

Hom.:

Bravo

AF:

0.00402

ESP6500AA

AF:

0.0181

AC:

ESP6500EA

AF:

0.00

AC:

ExAC

AF:

0.00137

AC:

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

SPATA13-related disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Aug 12, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.26

BayesDel_noAF

Benign

-0.14

Cadd

Benign

Dann

Uncertain

1.0

Eigen

Uncertain

0.25

Eigen_PC

Uncertain

0.28

FATHMM_MKL

Uncertain

0.95

MetaRNN

Benign

0.0068

T;T

MetaSVM

Uncertain

-0.052

MutationTaster

Benign

0.74

D;D

PrimateAI

Uncertain

0.53

Sift4G

Uncertain

0.021

D;D

Vest4

0.74

MVP

0.56

MPC

1.2

ClinPred

0.038

GERP RS

5.3

gMVP

0.44

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over